K-mer basierte Algorithmen in der Bioinformatik (S)

392219 Wittler Summer 2023 Wednesday 10:15-11:45 U10-146

(Je nach Wunsch/Bedarf der Studierenden wird das Seminar auf Deutsch oder Englisch durchgeführt.
Depending on the wishes/demands of the students, this seminar can be held in English or German.)

Based on original research papers, the participants will give oral presentations (20-45 min) and write short summaries (5-10 pages) about algorithmic problems in bioinformatics and their solutions. Talks and essays can be done in German or English. The first day covers an overview of possible topics, which will then be distributed to the students. Aspects of scientific writing and presenting will be covered as well.

The overarching topic of this semester are k-mers (a.k.a. q-grams). This simple concept builds a basis for many algorithmic solutions in bioinformatics, such as assembly, alignment, genome comparison, pangenomics, etc.

Possible concrete methods/publications to be presented/discussed in the seminar are:


De Bruijn Graphs

  • Holley, Guillaume, and Páll Melsted. “Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs.” Genome biology 21.1 (2020): 1-20.
  • Luhmann, Nina, Guillaume Holley, and Mark Achtman. “BlastFrost: fast querying of 100,000 s of bacterial genomes in Bifrost graphs.” Genome biology 22.1 (2021): 1-15.
  • Ekim, Barış, Bonnie Berger, and Rayan Chikhi. “Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.” Cell systems 12.10 (2021): 958-968.


Counting k-mers


05.04. Organization, topic selection, Scientific reading Slides: HowToRead
03.05. Scientific writing, introduction to LaTeX Notes on Scientific writing and citing, Latex-template, Bibtex-example (remove “.pdf” from filenames), Bibliography styles
10.05. Introductions, conclusions, math Notes 1, Notes 2, extended Latex-template (remove “.pdf” from filename)
24.05. Tables, figures, algorithms, Checklist on writing (1/2) extended Latex-template (remove “.pdf” from filename), checklist
07.06. Tables, figures, algorithms, Checklist on writing (2/2) extended Latex-template (remove “.pdf” from filename), checklist
14.06. N.V.: Altschul, Stephen F., et al. “Basic local alignment search tool.” (1990) paper
05.07. P.A.: Li, H. “Minimap2: pairwise alignment for nucleotide sequences.” (2018) paper